Author: bugman
Date: Tue Nov 24 16:48:38 2009
New Revision: 9930
URL: http://svn.gna.org/viewcvs/relax?rev=9930&view=rev
Log:
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
Modified:
1.3/specific_fns/api_base.py
Modified: 1.3/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/api_base.py?rev=9930&r1=9929&r2=9930&view=diff
==============================================================================
--- 1.3/specific_fns/api_base.py (original)
+++ 1.3/specific_fns/api_base.py Tue Nov 24 16:48:38 2009
@@ -125,6 +125,19 @@
raise RelaxImplementError
+ def deselect(self, model_index, sim_index=None):
+ """Deselect models or simulations.
+
+ @param model_index: The model index. This is zero for the
global models or equal to the global spin index (which covers the molecule,
residue, and spin indices).
+ @type model_index: int
+ @keyword sim_index: The optional Monte Carlo simulation index.
If None, then models will be deselected, otherwise the given simulation will.
+ @type sim_index: None or int
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def duplicate_data(self, pipe_from=None, pipe_to=None, model_index=None,
global_stats=False, verbose=True):
"""Duplicate the data specific to a single model.
@@ -146,6 +159,34 @@
def eliminate(self):
"""Dummy method for model elimination."""
+
+
+ def get_param_names(self, model_index=None):
+ """Return a vector of parameter names.
+
+ @keyword model_index: The model index. This is zero for the
global models or equal to the global spin index (which covers the molecule,
residue, and spin indices).
+ @type model_index: int
+ @return: The vector of parameter names.
+ @rtype: list of str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
+ def get_param_values(self, model_index=None, sim_index=None):
+ """Return a vector of parameter values.
+
+ @keyword model_index: The model index. This is zero for the
global models or equal to the global spin index (which covers the molecule,
residue, and spin indices).
+ @type model_index: int
+ @keyword sim_index: The optional Monte Carlo simulation index.
+ @type sim_index: int
+ @return: The vector of parameter values.
+ @rtype: list of str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
@@ -215,6 +256,21 @@
# Return the default of True.
return True
+
+
+ def map_bounds(self, param, spin_id=None):
+ """Create bounds for the OpenDX mapping function.
+
+ @param param: The name of the parameter to return the lower
and upper bounds of.
+ @type param: str
+ @param spin_id: The spin identification string.
+ @type spin_id: None or str
+ @return: The upper and lower bounds of the parameter.
+ @rtype: list of float
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def minimise(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, constraints=False, scaling=True,
verbosity=0, sim_index=None, lower=None, upper=None, inc=None):
@@ -250,6 +306,19 @@
raise RelaxImplementError
+ def model_desc(self, model_index):
+ """Return a description of the model.
+
+ @param model_index: The model index. This originates from the
model_loop().
+ @type model_index: int
+ @return: The model description.
+ @rtype: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def model_loop(self):
"""Default generator method for looping over the models.
@@ -293,6 +362,38 @@
raise RelaxImplementError
+ def model_type(self):
+ """Return the type of the model, either being 'local' or 'global'.
+
+ @return: The model type, one of 'local' or 'global'.
+ @rtype: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
+ def molmol_macro(self, param, style=None, colour_start=None,
colour_end=None, colour_list=None, spin_id=None):
+ """Create and return an array of Molmol macros.
+
+ @param param: The parameter name.
+ @type param: str
+ @keyword style: The Molmol style.
+ @type style: None or str
+ @keyword colour_start: The starting colour (must be a MOLMOL or X11
name).
+ @type colour_start: str
+ @keyword colour_end: The ending colour (must be a MOLMOL or X11
name).
+ @type colour_end: str
+ @keyword colour_list: The colour list used, either 'molmol' or
'x11'.
+ @type colour_list: str
+ @keyword spin_id: The spin identification string.
+ @type spin_id: str
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def num_instances(self):
"""Function for returning the number of instances.
@@ -312,6 +413,19 @@
def overfit_deselect(self):
"""Dummy function, nornally for deselecting spins with insufficient
data for minimisation."""
+
+
+ def read_columnar_results(self, file_data, verbosity=1):
+ """Read the columnar formatted results file.
+
+ @param file_data: The processed results file data.
+ @type file_data: list of lists of str
+ @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
+ @type verbosity: int
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
def return_conversion_factor(self, stat_type, spin=None, spin_id=None):
@@ -338,6 +452,21 @@
"""
return spin.relax_data
+
+
+ def return_data_desc(self, name, spin=None):
+ """Return a description of the spin specific object.
+
+ @param name: The name of the spin specific object.
+ @type name: str
+ @param spin: The spin container.
+ @type spin: SpinContainer instance
+ @return: The object description, or None.
+ @rtype: str or None
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
# Empty documentation string.
@@ -696,6 +825,19 @@
return spin.select_sim
+ def skip_function(self, model_index):
+ """Skip certain data.
+
+ @param model_index: The model index. This originates from the
model_loop().
+ @type model_index: int
+ @return: True if the data should be skipped, False
otherwise.
+ @rtype: bool
+ """
+
+ # Not implemented.
+ raise RelaxImplementError
+
+
def test_grid_ops(self, lower=None, upper=None, inc=None, n=None):
"""Function for testing that the grid search options are reasonable.
r9930 - /1.3/specific_fns/api_base.py